Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013951.1 Corchorus olitorius cultivar O-4 contig13984, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 32163
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:8218 original size:29 final size:28
Alignment explanation
Indices: 8146--8220 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
8136 CAAATTGACA
*
8146 TTTTGTCCCCTAAACTTTAATTTGGGAC
1 TTTTGCCCCCTAAACTTTAATTTGGGAC
* ****
8174 TTGTGCCAAAAAAAACTTTAATTTGGGAC
1 TTTTGCC-CCCTAAACTTTAATTTGGGAC
8203 GTTTTGCCCCCTAAACTT
1 -TTTTGCCCCCTAAACTT
8221 GCAATTTGAG
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
28 5 0.15
29 23 0.68
30 6 0.18
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (28 bp):
TTTTGCCCCCTAAACTTTAATTTGGGAC
Found at i:9177 original size:21 final size:21
Alignment explanation
Indices: 9153--9193 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9143 ACATTTATTA
*
9153 TAGAATATCAATTTGTGGTTG
1 TAGAAAATCAATTTGTGGTTG
9174 TAGAAAATCAATTTGTGGTT
1 TAGAAAATCAATTTGTGGTT
9194 ATGATGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (21 bp):
TAGAAAATCAATTTGTGGTTG
Found at i:9518 original size:1 final size:1
Alignment explanation
Indices: 9512--9536 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9502 GCTAGAACTC
9512 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
9537 CTAGCTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11226 original size:6 final size:6
Alignment explanation
Indices: 11217--11241 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11207 TCGTCGCCGC
11217 CGCCAT CGCCAT CGCCAT CGCCAT C
1 CGCCAT CGCCAT CGCCAT CGCCAT C
11242 ACTAGAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CGCCAT
Found at i:19103 original size:22 final size:22
Alignment explanation
Indices: 19078--19124 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19068 TTTTTAATTG
*
19078 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
19100 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
19122 AGT
1 AGT
19125 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:19103 original size:93 final size:93
Alignment explanation
Indices: 19001--19185 Score: 289
Period size: 93 Copynumber: 2.0 Consensus size: 93
18991 GCTTTTAAAT
* * * *
19001 TAAATTAGTAATATCGTAAAAATAAAATTGGTATACGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
19066 AGTTTTTAATTGAGTAAAACTATAAAAG
66 AGTTTTTAATTGAGTAAAACTATAAAAG
* * *
19094 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTCGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
* *
19159 AGTTTTTAGTTGATTAAAACTATAAAA
66 AGTTTTTAATTGAGTAAAACTATAAAA
19186 ATTTAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAATTGAGTAAAACTATAAAAG
Found at i:20414 original size:5 final size:5
Alignment explanation
Indices: 20404--20473 Score: 80
Period size: 5 Copynumber: 15.2 Consensus size: 5
20394 TATAATAGTA
*
20404 ATAAG ATAAG AT-AG -TAAG ATAAG ATAAG AT-AG -TAAG AT-AG -TAAA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG
*
20448 ATAAG ATAAG ATAAG ATAGG ATAAG A
1 ATAAG ATAAG ATAAG ATAAG ATAAG A
20474 GTACACTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 3 0.05
4 11 0.20
5 41 0.75
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (5 bp):
ATAAG
Found at i:20427 original size:18 final size:18
Alignment explanation
Indices: 20404--20466 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
20394 TATAATAGTA
20404 ATAAGATAAGATAGTAAG
1 ATAAGATAAGATAGTAAG
20422 ATAAGATAAGATAGTAAG
1 ATAAGATAAGATAGTAAG
20440 AT-AG-TAA-A-A-TAAG
1 ATAAGATAAGATAGTAAG
20453 ATAAGATAAGATAG
1 ATAAGATAAGATAG
20467 GATAAGAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.15
14 3 0.08
15 4 0.10
16 4 0.10
17 3 0.08
18 20 0.50
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.22
Consensus pattern (18 bp):
ATAAGATAAGATAGTAAG
Found at i:20443 original size:26 final size:26
Alignment explanation
Indices: 20410--20460 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20400 AGTAATAAGA
*
20410 TAAGATAGTAAGATAAGATAAGATAG
1 TAAGATAGTAAAATAAGATAAGATAG
20436 TAAGATAGTAAAATAAGATAAGATA
1 TAAGATAGTAAAATAAGATAAGATA
20461 AGATAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.24
Consensus pattern (26 bp):
TAAGATAGTAAAATAAGATAAGATAG
Found at i:28894 original size:57 final size:57
Alignment explanation
Indices: 28786--28899 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
28776 ATTAATCAAA
*
28786 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCAT-AAAAAAGACGTTTTAGGACCAAGGCT
* * * * *
28844 TATCGAGTGACATATTTTTTTATTAGATGCCT-AAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACAT-GTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC
28900 ATGATGCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
57 22 0.45
58 12 0.24
59 15 0.31
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (57 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:30892 original size:39 final size:40
Alignment explanation
Indices: 30837--30917 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
30827 ATACCTAAGA
* *
30837 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
*
30876 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
30916 AT
1 AT
30918 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
Found at i:31553 original size:21 final size:21
Alignment explanation
Indices: 31529--31569 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31519 TGGAGTTGTG
31529 AGATTAAACACTGTACAGATC
1 AGATTAAACACTGTACAGATC
***
31550 AGATTAGTTACTGTACAGAT
1 AGATTAAACACTGTACAGAT
31570 GGGCGATAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (21 bp):
AGATTAAACACTGTACAGATC
Done.